paper-repro-python

# Follow this workflow end-to-end unless the user explicitly asks to skip steps

## 1) Intake and scope

- Confirm input artifacts: TeX source path(s), PDF path, supplementary files, target repository, and expected outputs.
- State assumptions explicitly when information is missing.
- Keep approach adaptable to the specific paper; do not force a fixed dependency stack or rigid project template.
- Check whether the working folder already contains paper source files (`.tex`, `.bib`, style files, figures).
- Source priority rule:
  - If usable TeX source files are present, use TeX as the primary source for reproduction.
  - If TeX is absent or incomplete for key content, fall back to PDF extraction only for missing parts.

## 2) Source extraction (TeX-first, PDF fallback)

- TeX-first path (preferred):
  - Parse and read the main TeX project structure first (`main.tex` or equivalent entry file and includes).
  - Preserve original scientific wording when converting relevant content to Markdown notes.
  - Resolve equations, theorem blocks, citations, and appendices from source files whenever possible.
  - Record unresolved include/bibliography issues explicitly; do not invent missing content.

- PDF fallback path (required when TeX is unavailable/incomplete):
  - Extract paper content page by page into Markdown, preserving the original wording.
  - Do not summarize, paraphrase, or rewrite scientific statements.
  - Preserve structure faithfully:
    - Title, authors, affiliations, abstract, sections, subsections.
    - Equations (LaTeX-friendly when possible), theorem/lemma/proposition blocks.
    - Tables, figure captions, references, appendices, footnotes.
  - If a PDF is scanned or partially unreadable:
    - Run OCR and mark uncertain spans clearly.
    - Never silently invent missing text.
  - Include image references/placeholders when figures cannot be represented as plain text.
  - Produce one primary output file such as `paper_fulltext.md`.

## 3) Extraction qual...